rtDetect: Detecting retrotranscript insertion in nuclear genomes.

In PapenfussLab/svaRetro: Retrotransposed transcript detection from structural variants

Detecting retrotranscript insertion in nuclear genomes.

Description

Detecting retrotranscript insertion in nuclear genomes.

Usage

rtDetect(gr, genes, maxgap = 100, minscore = 0.4)

Arguments

gr	A GRanges object
genes	TxDb object of genes. hg19 and hg38 are supported in the current version.
maxgap	The maxium distance allowed on the reference genome between the paired exon boundries.
minscore	The minimum proportion of intronic deletions of a transcript should be identified.

Details

This function searches for retroposed transcripts by identifying breakpoints supporting intronic deletions and fusions between exons and remote loci. Only BND notations are supported at the current stage.

Value

A GRangesList object, named insSite and rt, reporting breakpoints supporting insert sites and retroposed transcripts respectively. 'exon' and 'txs' in the metadata columns report exon_id and transcript_name from the 'genes' object.

Examples

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
genes <- TxDb.Hsapiens.UCSC.hg19.knownGene
vcf.file <- system.file("extdata", "diploidSV.vcf",
                         package = "svaRetro")
vcf <- VariantAnnotation::readVcf(vcf.file, "hg19")
gr <- breakpointRanges(vcf, nominalPosition=TRUE)
rt <- rtDetect(gr, genes, maxgap=30, minscore=0.6)

PapenfussLab/svaRetro documentation built on June 15, 2022, 1:42 a.m.